Before responding to your questions in turn, I'd like to propose that I think this issue behaves somewhat like the (justifiably) maligned Laffer curve. In other words, I think it's clear that with no education, humans would still be stuck in primitive societies, which were sustainable, and involved small per capita resource usage. As education increases, you do get an increase in resource consumption, with a standard-of-living increase. However, I believe that in the future, we can achieve lower levels of resource consumption again, with further increases in education.
More time living alone means more energy consumption.
Staying in school doesn't just mean "living alone". It probably also means living modestly, in a small apartment. And it often does mean living with roommates. The people at both the universities I went to (in the US) all lived with small energy and spatial footprints, relative to working adults in the surrounding society. So, I'd say this issue favors staying in school, as more sustainable.
A link on CO2 footprint vs. age that reflects this issue, although school vs. work at the same age is not teased apart.
Fewer children may have both positive and negative effects.
While, technically this is true (there are positive and negative effects), I strongly disagree with the implied equivalency. Human beings consume lots of resources. Lots. In those countries where higher education is a realistic option (as posed in your question), humans consume even more resources. More humans fundamentally means more resource consumption. Not to mention the basic math that birth rates above the replacement rate are inherently unsustainable, as long as we're bound to this one planet.
Less career time means less overall energy available for manual production.
Exactly. As I alluded to earlier, students do have lower environmental footprints than an average working adult. The amount of work output by today's current population vastly exceeds that required to fulfill basic human needs (as evidenced by many of us working in jobs that are not fundamentally necessary). We need people to be working at jobs less than they do now (in the developed world), and producing less. I'm not advocating education simply on the grounds that it takes time away from production, but I do believe that's a beneficial side effect.
and the labor is automated via cheap energy sources like fossil fuels. This leads to less flexibility regarding reducing energy usage.
Labor will be automated regardless, and less educated workers could actually provide more incentive to automate. I've seen a number of your posts on the site that suggest to me that you think automation fundamentally increases energy usage. While that could be its own separate discussion, I'll merely assert here that I find that to be false (and my apologies if that's not actually your belief).
Less time and flexibility to make informed choices regarding sustainability because of additional burdens like student loans requiring additional efforts to make ends meet.
First of all, you can't make informed choices without education. Education underlies all decision-making. If there's any obstacle to sustainability today in the US (where I live), it's ignorance of the basic science that supports consensus thinking on climate change. While there are educated skeptics who simply don't trust climate science, want more data, or believe the solution is elsewhere (not sustainability, but something like geoengineering), the majority here are skeptical because of a lack of basic understanding of the science. I believe a subject like this, while possible to treat at the high school level, is probably better expanded on at universities.
Finally, at least in the US, it's not true that taking out student loans requires working more to make ends meet. It's precisely the opposite. Higher levels of education reap higher lifetime earnings by an amount that easily pays for the cost of the extra education (plus interest). Granted, that equation is going to be different in every country, as tuition rates vary, as do student loan interest rates. But, based simply on the example of the world's largest developed economy, you do not wind up having to work more simply because you paid for more education. You may choose to work more, because you have a more enjoyable career, or have suffered less wear-and-tear from a white collar career. But, that's a separate point.